Single HiC QC report

Processing

 Run time
 Started @ 2023-05-22 12:14:05
 Finished @ 2023-05-22 12:14:29
 Duration: 0 days, 00h 00min 24s

 Processing directory
 /__w/HiCool/HiCool/docs/reference

 Reads location
 R1: /github/home/.cache/R/ExperimentHub/1fe971273e9d_7833
 R2: /github/home/.cache/R/ExperimentHub/1fe923fbe457_7834

 Genome reference
 /tmp/RtmpLG33tZ/R64-1-1

Command

x <- HiCool::HiCool(
    r1 = "/github/home/.cache/R/ExperimentHub/1fe971273e9d_7833",
    r2 = "/github/home/.cache/R/ExperimentHub/1fe923fbe457_7834",
    genome = "/tmp/RtmpLG33tZ/R64-1-1",
    resolutions = NA,
    restriction = "DpnII,HinfI",
    iterative = TRUE,
    balancing_args = " --min-nnz 10 --mad-max 5 ",
    threads = 1,
    output = "./HiCool/",
    exclude_chr = "Mito|chrM|MT",
    keep_bam = FALSE,
    scratch = "/tmp/RtmpLG33tZ"
)

 Generated HiCExperiment object

x
## CoolFile object
## .mcool file: /__w/HiCool/HiCool/docs/reference/HiCool/matrices/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.mcool 
## resolution: 1000 
## pairs file: /__w/HiCool/HiCool/docs/reference/HiCool/pairs/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.pairs 
## metadata(3): log stats args
import(x)
## `HiCExperiment` object with 60,836 contacts over 12,079 regions 
## -------
## fileName: "/__w/HiCool/HiCool/docs/reference/HiCool/matrices/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.mcool" 
## focus: "whole genome" 
## resolutions(5): 1000 2000 4000 8000 16000
## active resolution: 1000 
## interactions: 56522 
## scores(2): count balanced 
## topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) 
## pairsFile: /__w/HiCool/HiCool/docs/reference/HiCool/pairs/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.pairs 
## metadata(3): log stats args

Mapping results

Number of paired-end fragments 100,000
Total number of pairs after mapping 73,993
Number of valid pairs 61,678 (83.36% of all pairs)
Number of unique valid pairs 60,959 (82.38% of all pairs)
Number of pairs from uncut fragments (+-) 10,027 (13.55% of all pairs)
Number of pairs from self-religated fragments (-+) 2,205 (2.98% of all pairs)
Number of dumped pairs (– or ++) 83 (0.11% of all pairs)

 Minimum # of restriction sites to retain `+-` pairs: 7
 Minimum # of restriction sites to retain `-+` pairs: 7

Log file content

## HiCool working directory ::: /__w/HiCool/HiCool/docs/reference
## HiCool argument ::: r1: /github/home/.cache/R/ExperimentHub/1fe971273e9d_7833
## HiCool argument ::: r2: /github/home/.cache/R/ExperimentHub/1fe923fbe457_7834
## HiCool argument ::: genome: /tmp/RtmpLG33tZ/R64-1-1
## HiCool argument ::: resolutions: 
## HiCool argument ::: restriction: DpnII,HinfI
## HiCool argument ::: iterative: TRUE
## HiCool argument ::: balancing_args:  --min-nnz 10 --mad-max 5 
## HiCool argument ::: threads: 1
## HiCool argument ::: output: ./HiCool/
## HiCool argument ::: exclude_chr: Mito|chrM|MT
## HiCool argument ::: keep_bam: FALSE
## HiCool argument ::: scratch: /tmp/RtmpLG33tZ
## ----------------
## ## hicstuff: v3.1.5 log file
## ## date: 2023-05-22 12:14:05
## ## enzyme: DpnII,HinfI
## ## input1: /github/home/.cache/R/ExperimentHub/1fe971273e9d_7833 
## ## input2: /github/home/.cache/R/ExperimentHub/1fe923fbe457_7834
## ## ref: /tmp/RtmpLG33tZ/R64-1-1
## ---
## 2023-05-22,12:14:08 :: INFO :: 100000 reads to parse
## 2023-05-22,12:14:08 :: INFO :: Truncating unaligned reads to 20bp and mapping.
## 2023-05-22,12:14:11 :: INFO :: 19256 reads left to map.
## 2023-05-22,12:14:11 :: INFO :: Trying to map unaligned reads at full length (35bp).
## 2023-05-22,12:14:12 :: INFO :: 18387 reads left to map.
## 2023-05-22,12:14:12 :: INFO :: 81613 reads aligned / 100000 total reads.
## 2023-05-22,12:14:13 :: INFO :: 100000 reads to parse
## 2023-05-22,12:14:13 :: INFO :: Truncating unaligned reads to 20bp and mapping.
## 2023-05-22,12:14:16 :: INFO :: 20617 reads left to map.
## 2023-05-22,12:14:16 :: INFO :: Trying to map unaligned reads at full length (35bp).
## 2023-05-22,12:14:16 :: INFO :: 19373 reads left to map.
## 2023-05-22,12:14:17 :: INFO :: 80627 reads aligned / 100000 total reads.
## 2023-05-22,12:14:21 :: INFO :: 81% reads (single ends) mapped with Q >= 10.0 (162240/200000)
## 2023-05-22,12:14:24 :: INFO :: Filtering with thresholds: uncuts=7 loops=7
## 2023-05-22,12:14:25 :: INFO :: Proportion of inter contacts: 22.03% (intra: 48089, inter: 13589)
## 2023-05-22,12:14:25 :: INFO :: 12315 pairs discarded: Loops: 2205, Uncuts: 10027, Weirds: 83
## 2023-05-22,12:14:25 :: INFO :: 61678 pairs kept (83.36%)
## 2023-05-22,12:14:27 :: INFO :: 1% PCR duplicates have been filtered out (719 / 61678 pairs) 
## 2023-05-22,12:14:29 :: INFO :: Contact map generated after 0h 0m 23s

Session information

System

## OS:              Ubuntu 22.04.2 LTS
## system:          x86_64, linux-gnu
## UI:              X11
## R:               4.3.0(/usr/local/lib/R)
## Python:          3.7.12(/github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/bin/python)
## Bioconductor:    3.18
## basilisk:        1.13.0
## HiCExperiment:   1.1.0
## HiCool:          1.1.0

System packages

## samtools:    1.16.1
## bowtie2:     2.5.0

R packages

##  package                * version   date (UTC) lib source
##  AnnotationDbi            1.63.1    2023-05-02 [1] Bioconductor
##  AnnotationHub          * 3.9.1     2023-05-01 [1] Bioconductor
##  basilisk                 1.13.0    2023-05-19 [1] Bioconductor
##  basilisk.utils           1.13.1    2023-05-19 [1] Bioconductor
##  Biobase                  2.61.0    2023-04-25 [1] Bioconductor
##  BiocFileCache          * 2.9.0     2023-04-25 [1] Bioconductor
##  BiocGenerics           * 0.47.0    2023-04-25 [1] Bioconductor
##  BiocIO                   1.11.0    2023-04-25 [1] Bioconductor
##  BiocManager              1.30.20   2023-02-24 [2] CRAN (R 4.3.0)
##  BiocParallel             1.35.1    2023-05-05 [1] Bioconductor
##  BiocVersion              3.18.0    2023-04-25 [2] Bioconductor
##  Biostrings               2.69.1    2023-05-16 [1] Bioconductor
##  bit                      4.0.5     2022-11-15 [1] CRAN (R 4.3.0)
##  bit64                    4.0.5     2020-08-30 [1] CRAN (R 4.3.0)
##  bitops                   1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
##  blob                     1.2.4     2023-03-17 [1] CRAN (R 4.3.0)
##  bookdown                 0.34      2023-05-09 [1] CRAN (R 4.3.0)
##  bslib                    0.4.2     2022-12-16 [2] CRAN (R 4.3.0)
##  cachem                   1.0.8     2023-05-01 [2] CRAN (R 4.3.0)
##  cli                      3.6.1     2023-03-23 [2] CRAN (R 4.3.0)
##  codetools                0.2-19    2023-02-01 [3] CRAN (R 4.3.0)
##  colorspace               2.1-0     2023-01-23 [1] CRAN (R 4.3.0)
##  crayon                   1.5.2     2022-09-29 [2] CRAN (R 4.3.0)
##  crosstalk                1.2.0     2021-11-04 [1] CRAN (R 4.3.0)
##  curl                     5.0.0     2023-01-12 [2] CRAN (R 4.3.0)
##  data.table               1.14.8    2023-02-17 [1] CRAN (R 4.3.0)
##  DBI                      1.1.3     2022-06-18 [1] CRAN (R 4.3.0)
##  dbplyr                 * 2.3.2     2023-03-21 [1] CRAN (R 4.3.0)
##  DelayedArray             0.27.3    2023-05-17 [1] Bioconductor
##  desc                     1.4.2     2022-09-08 [2] CRAN (R 4.3.0)
##  digest                   0.6.31    2022-12-11 [2] CRAN (R 4.3.0)
##  dir.expiry               1.9.0     2023-04-25 [1] Bioconductor
##  downlit                  0.4.2     2022-07-05 [2] CRAN (R 4.3.0)
##  dplyr                    1.1.2     2023-04-20 [1] CRAN (R 4.3.0)
##  ellipsis                 0.3.2     2021-04-29 [2] CRAN (R 4.3.0)
##  evaluate                 0.21      2023-05-05 [2] CRAN (R 4.3.0)
##  ExperimentHub          * 2.7.1     2023-04-23 [1] Bioconductor
##  fansi                    1.0.4     2023-01-22 [2] CRAN (R 4.3.0)
##  fastmap                  1.1.1     2023-02-24 [2] CRAN (R 4.3.0)
##  filelock                 1.0.2     2018-10-05 [1] CRAN (R 4.3.0)
##  fs                       1.6.2     2023-04-25 [2] CRAN (R 4.3.0)
##  generics                 0.1.3     2022-07-05 [1] CRAN (R 4.3.0)
##  GenomeInfoDb             1.37.1    2023-05-04 [1] Bioconductor
##  GenomeInfoDbData         1.2.10    2023-05-11 [1] Bioconductor
##  GenomicRanges            1.53.1    2023-05-04 [1] Bioconductor
##  ggplot2                  3.4.2     2023-04-03 [1] CRAN (R 4.3.0)
##  glue                     1.6.2     2022-02-24 [2] CRAN (R 4.3.0)
##  gtable                   0.3.3     2023-03-21 [1] CRAN (R 4.3.0)
##  here                     1.0.1     2020-12-13 [1] CRAN (R 4.3.0)
##  HiCExperiment          * 1.1.0     2023-04-25 [1] Bioconductor
##  HiContactsData         * 1.3.0     2023-04-27 [1] Bioconductor
##  HiCool                 * 1.1.0     2023-05-22 [1] Bioconductor
##  htmltools                0.5.5     2023-03-23 [2] CRAN (R 4.3.0)
##  htmlwidgets              1.6.2     2023-03-17 [2] CRAN (R 4.3.0)
##  httpuv                   1.6.11    2023-05-11 [2] CRAN (R 4.3.0)
##  httr                     1.4.6     2023-05-08 [2] CRAN (R 4.3.0)
##  InteractionSet           1.29.0    2023-04-25 [1] Bioconductor
##  interactiveDisplayBase   1.39.0    2023-04-25 [1] Bioconductor
##  IRanges                  2.35.1    2023-05-03 [1] Bioconductor
##  jquerylib                0.1.4     2021-04-26 [2] CRAN (R 4.3.0)
##  jsonlite                 1.8.4     2022-12-06 [2] CRAN (R 4.3.0)
##  KEGGREST                 1.41.0    2023-04-25 [1] Bioconductor
##  knitr                    1.42      2023-01-25 [2] CRAN (R 4.3.0)
##  later                    1.3.1     2023-05-02 [2] CRAN (R 4.3.0)
##  lattice                  0.21-8    2023-04-05 [3] CRAN (R 4.3.0)
##  lazyeval                 0.2.2     2019-03-15 [1] CRAN (R 4.3.0)
##  lifecycle                1.0.3     2022-10-07 [2] CRAN (R 4.3.0)
##  magrittr                 2.0.3     2022-03-30 [2] CRAN (R 4.3.0)
##  Matrix                   1.5-4.1   2023-05-18 [2] CRAN (R 4.3.0)
##  MatrixGenerics           1.13.0    2023-04-25 [1] Bioconductor
##  matrixStats              0.63.0    2022-11-18 [1] CRAN (R 4.3.0)
##  memoise                  2.0.1     2021-11-26 [2] CRAN (R 4.3.0)
##  mime                     0.12      2021-09-28 [2] CRAN (R 4.3.0)
##  munsell                  0.5.0     2018-06-12 [1] CRAN (R 4.3.0)
##  pillar                   1.9.0     2023-03-22 [2] CRAN (R 4.3.0)
##  pkgconfig                2.0.3     2019-09-22 [2] CRAN (R 4.3.0)
##  pkgdown                  2.0.7     2022-12-14 [1] CRAN (R 4.3.0)
##  plotly                   4.10.1    2022-11-07 [1] CRAN (R 4.3.0)
##  png                      0.1-8     2022-11-29 [1] CRAN (R 4.3.0)
##  promises                 1.2.0.1   2021-02-11 [2] CRAN (R 4.3.0)
##  purrr                    1.0.1     2023-01-10 [2] CRAN (R 4.3.0)
##  R6                       2.5.1     2021-08-19 [2] CRAN (R 4.3.0)
##  ragg                     1.2.5     2023-01-12 [2] CRAN (R 4.3.0)
##  rappdirs                 0.3.3     2021-01-31 [2] CRAN (R 4.3.0)
##  Rcpp                     1.0.10    2023-01-22 [2] CRAN (R 4.3.0)
##  RCurl                    1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
##  reticulate               1.28      2023-01-27 [1] CRAN (R 4.3.0)
##  rhdf5                    2.45.0    2023-04-25 [1] Bioconductor
##  rhdf5filters             1.13.2    2023-04-30 [1] Bioconductor
##  Rhdf5lib                 1.23.0    2023-04-25 [1] Bioconductor
##  rlang                    1.1.1     2023-04-28 [2] CRAN (R 4.3.0)
##  rmarkdown                2.21      2023-03-26 [2] CRAN (R 4.3.0)
##  rmdformats               1.0.4     2022-05-17 [1] CRAN (R 4.3.0)
##  rprojroot                2.0.3     2022-04-02 [2] CRAN (R 4.3.0)
##  RSQLite                  2.3.1     2023-04-03 [1] CRAN (R 4.3.0)
##  rstudioapi               0.14      2022-08-22 [2] CRAN (R 4.3.0)
##  S4Arrays                 1.1.4     2023-05-14 [1] Bioconductor
##  S4Vectors                0.39.1    2023-05-03 [1] Bioconductor
##  sass                     0.4.6     2023-05-03 [2] CRAN (R 4.3.0)
##  scales                   1.2.1     2022-08-20 [1] CRAN (R 4.3.0)
##  sessioninfo              1.2.2     2021-12-06 [2] CRAN (R 4.3.0)
##  shiny                    1.7.4     2022-12-15 [2] CRAN (R 4.3.0)
##  SparseArray              1.1.5     2023-05-17 [1] Bioconductor
##  strawr                   0.0.91    2023-03-29 [1] CRAN (R 4.3.0)
##  stringi                  1.7.12    2023-01-11 [2] CRAN (R 4.3.0)
##  stringr                  1.5.0     2022-12-02 [2] CRAN (R 4.3.0)
##  SummarizedExperiment     1.31.1    2023-05-01 [1] Bioconductor
##  systemfonts              1.0.4     2022-02-11 [2] CRAN (R 4.3.0)
##  textshaping              0.3.6     2021-10-13 [2] CRAN (R 4.3.0)
##  tibble                   3.2.1     2023-03-20 [2] CRAN (R 4.3.0)
##  tidyr                    1.3.0     2023-01-24 [1] CRAN (R 4.3.0)
##  tidyselect               1.2.0     2022-10-10 [1] CRAN (R 4.3.0)
##  tzdb                     0.4.0     2023-05-12 [1] CRAN (R 4.3.0)
##  utf8                     1.2.3     2023-01-31 [2] CRAN (R 4.3.0)
##  vctrs                    0.6.2     2023-04-19 [2] CRAN (R 4.3.0)
##  viridisLite              0.4.2     2023-05-02 [1] CRAN (R 4.3.0)
##  vroom                    1.6.3     2023-04-28 [1] CRAN (R 4.3.0)
##  whisker                  0.4.1     2022-12-05 [2] CRAN (R 4.3.0)
##  withr                    2.5.0     2022-03-03 [2] CRAN (R 4.3.0)
##  xfun                     0.39      2023-04-20 [2] CRAN (R 4.3.0)
##  xml2                     1.3.4     2023-04-27 [2] CRAN (R 4.3.0)
##  xtable                   1.8-4     2019-04-21 [2] CRAN (R 4.3.0)
##  XVector                  0.41.1    2023-05-03 [1] Bioconductor
##  yaml                     2.3.7     2023-01-23 [2] CRAN (R 4.3.0)
##  zlibbioc                 1.47.0    2023-04-25 [1] Bioconductor
## 
##  [1] /__w/_temp/Library
##  [2] /usr/local/lib/R/site-library
##  [3] /usr/local/lib/R/library

Python environment

##  python:         /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/bin/python
##  libpython:      /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/lib/libpython3.7m.so
##  pythonhome:     /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env:/github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env
##  version:        3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53)  [GCC 9.4.0]
##  numpy:          /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/lib/python3.7/site-packages/numpy
##  numpy_version:  1.21.6
##  
##  NOTE: Python version was forced by use_python function

Python packages

##                            full              package
## 1              asciitree==0.3.3            asciitree
## 2                 attrs==23.1.0                attrs
## 3               biopython==1.79            biopython
## 4                  bokeh==2.4.3                bokeh
## 5             Bottleneck==1.3.5           Bottleneck
## 6               brotlipy==0.7.0             brotlipy
## 7        cached-property==1.5.2      cached-property
## 8             certifi==2023.5.7              certifi
## 9                  cffi==1.15.1                 cffi
## 10    charset-normalizer==3.1.0   charset-normalizer
## 11           chromosight==1.6.3          chromosight
## 12                 click==8.1.3                click
## 13           cloudpickle==2.2.1          cloudpickle
## 14                cooler==0.9.1               cooler
## 15         cryptography==38.0.2         cryptography
## 16               cycler==0.11.0               cycler
## 17              cytoolz==0.12.0              cytoolz
## 18              dask==2021.10.0                 dask
## 19                  dill==0.3.6                 dill
## 20       distributed==2021.10.0          distributed
## 21                docopt==0.6.2               docopt
## 22            fonttools==4.38.0            fonttools
## 23             fsspec==2023.1.0               fsspec
## 24                  h5py==3.7.0                 h5py
## 25              HeapDict==1.0.1             HeapDict
## 26              hicstuff==3.1.5             hicstuff
## 27                    idna==3.4                 idna
## 28   importlib-metadata==4.11.4   importlib-metadata
## 29  importlib-resources==5.12.0  importlib-resources
## 30                Jinja2==3.1.2               Jinja2
## 31                joblib==1.2.0               joblib
## 32           jsonschema==4.17.3           jsonschema
## 33            kiwisolver==1.4.4           kiwisolver
## 34                locket==1.0.0               locket
## 35            MarkupSafe==2.1.1           MarkupSafe
## 36            matplotlib==3.5.3           matplotlib
## 37               msgpack==1.0.4              msgpack
## 38        multiprocess==0.70.14         multiprocess
## 39               munkres==1.1.4              munkres
## 40               numexpr==2.8.3              numexpr
## 41                numpy==1.21.6                numpy
## 42              packaging==23.1            packaging
## 43                pandas==1.3.5               pandas
## 44                 partd==1.4.0                partd
## 45                Pillow==9.2.0               Pillow
## 46                  pip==23.1.2                  pip
## 47 pkgutil_resolve_name==1.3.10 pkgutil_resolve_name
## 48                psutil==5.9.3               psutil
## 49              pycparser==2.21            pycparser
## 50             pyfaidx==0.7.2.1              pyfaidx
## 51               pyfastx==1.1.0              pyfastx
## 52            pyOpenSSL==23.1.1            pyOpenSSL
## 53              pypairix==0.3.7             pypairix
## 54             pyparsing==3.0.9            pyparsing
## 55           pyrsistent==0.18.1           pyrsistent
## 56                pysam==0.21.0                pysam
## 57               PySocks==1.7.1              PySocks
## 58       python-dateutil==2.8.2      python-dateutil
## 59                 pytz==2023.3                 pytz
## 60                PyVCF3==1.0.3               PyVCF3
## 61                  PyYAML==6.0               PyYAML
## 62             requests==2.29.0             requests
## 63          scikit-learn==1.0.2         scikit-learn
## 64                 scipy==1.7.3                scipy
## 65           setuptools==67.7.2           setuptools
## 66           simplejson==3.17.6           simplejson
## 67                  six==1.16.0                  six
## 68      sortedcontainers==2.4.0     sortedcontainers
## 69                 tblib==1.7.0                tblib
## 70         threadpoolctl==3.1.0        threadpoolctl
## 71                toolz==0.12.0                toolz
## 72                 tornado==6.2              tornado
## 73     typing_extensions==4.5.0    typing_extensions
## 74         unicodedata2==14.0.0         unicodedata2
## 75             urllib3==1.26.15              urllib3
## 76                wheel==0.40.0                wheel
## 77                  zict==2.2.0                 zict
## 78                 zipp==3.15.0                 zipp